Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011778592.1 MVAN_RS06715 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000015305.1:WP_011778592.1 Length = 483 Score = 250 bits (638), Expect = 9e-71 Identities = 161/464 (34%), Positives = 235/464 (50%), Gaps = 25/464 (5%) Query: 41 YIGGEWVDTKE--RMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98 YIGG WV + NP+ P++V+GT + + A++A KA W E R Sbjct: 7 YIGGAWVPAQSGRTFTRANPADPADVIGTFPASDADDVRNAVDALEKAAPEWAATAPERR 66 Query: 99 SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158 + +L AAA + R L A LV E GK EA+ +V + +YA A R Sbjct: 67 ASILESAAAQLESRSEALIAELVREEGKTVAEATMEVTRTPSNLRFYAAEATR-----AA 121 Query: 159 VVPYPGEDNESFYV---PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVV 215 + +P + Y P+G I PWNFP+ I + + +AVG+ V+ KP+E ++ Sbjct: 122 GMTFPAAGDTMVYTVREPVGIVGAITPWNFPLNIPSRKLGPALAVGDPVLFKPSELTPLM 181 Query: 216 GAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRL 275 G ++ E G PPGV+ + G G GA + R + FTGS VG I+ A G Sbjct: 182 GQRLVEALLAGGLPPGVLALVHGDGV-AGAAVAADERVAAVTFTGSTAVGRSIHRAVGP- 239 Query: 276 APGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAY 335 +R +E GGK+ ++V + AD D AA +V A+G GQ C+ SR+I T + Sbjct: 240 ------HRRVQLEMGGKNPVVVADDADLDRAAALIVKGAFGLSGQACTGTSRVIATDATH 293 Query: 336 EPVLERVLKRAERLSVGP-AEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLE 393 + ++ERV+ RAE L VGP A+ D+G + SA Q K Y+ +G +EG L GG RL+ Sbjct: 294 DGLVERVVARAEALRVGPGAQPGIDMGALASAAQAEKFAHYVGVGVDEGASLRCGGTRLD 353 Query: 394 ----GEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449 G+F+ P VFT+ P RI EE+FGP+L+ R EA+E+AN T +GL+ + Sbjct: 354 VPGHAGGFFVRPAVFTDTEPTMRIVSEEVFGPLLAFQRAGSLTEAIELANATEFGLSAAI 413 Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGT 493 + RE G + N+ TG + PFGG+K S T Sbjct: 414 VTGDLATAAQFARESRTGLVKINQPTTGMAMNA-PFGGYKASST 456 Lambda K H 0.319 0.137 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 598 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 516 Length of database: 483 Length adjustment: 34 Effective length of query: 482 Effective length of database: 449 Effective search space: 216418 Effective search space used: 216418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory